3gpl: Difference between revisions

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 ==Crystal structure of the ternary complex of RecD2 with DNA and ADPNP==
-<StructureSection load='3gpl' size='340' side='right' caption='[[3gpl]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='3gpl' size='340' side='right'caption='[[3gpl]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3gpl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GPL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3gpl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GPL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gp8|3gp8]], [[3e1s|3e1s]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_1902, recD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpl OCA], [https://pdbe.org/3gpl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gpl RCSB], [https://www.ebi.ac.uk/pdbsum/3gpl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpl ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpl OCA], [http://pdbe.org/3gpl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpl RCSB], [http://www.ebi.ac.uk/pdbsum/3gpl PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RECDL_DEIRA RECDL_DEIRA]] DNA-dependent ATPase (ssDNA better than dsDNA) and ATP-dependent 5'-3' DNA helicase. Appears to move along DNA in single base steps, powered by hydrolysis of 1 molecule of ATP. Has low processivity; short (20 bp) substrates with 5'-overhangs or forked ends are the best substrates, is much less efficient on 52 or 76 bp substrates with 5'- overhangs. The presence of single-stranded DNA-binding protein (SSB) increases unwinding 4-5 fold. Has no activity on blunt DNA or DNA with 3'-overhangs. Requires at least 10 bases of 5'-ssDNA for helicase activity.<ref>PMID:15466873</ref> <ref>PMID:19490894</ref>
+[https://www.uniprot.org/uniprot/RECDL_DEIRA RECDL_DEIRA] DNA-dependent ATPase (ssDNA better than dsDNA) and ATP-dependent 5'-3' DNA helicase. Appears to move along DNA in single base steps, powered by hydrolysis of 1 molecule of ATP. Has low processivity; short (20 bp) substrates with 5'-overhangs or forked ends are the best substrates, is much less efficient on 52 or 76 bp substrates with 5'- overhangs. The presence of single-stranded DNA-binding protein (SSB) increases unwinding 4-5 fold. Has no activity on blunt DNA or DNA with 3'-overhangs. Requires at least 10 bases of 5'-ssDNA for helicase activity.<ref>PMID:15466873</ref> <ref>PMID:19490894</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/3gpl_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/3gpl_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Exonuclease|Exonuclease]]
+*[[Exonuclease 3D structures|Exonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Deira]]
+[[Category: Deinococcus radiodurans R1]]
-[[Category: Cook, N]]
+[[Category: Large Structures]]
-[[Category: Saikrishnan, K]]
+[[Category: Cook N]]
-[[Category: Wigley, D B]]
+[[Category: Saikrishnan K]]
-[[Category: Alpha and beta protein]]
+[[Category: Wigley DB]]
-[[Category: Atp-binding]]
-[[Category: Helicase]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Nucleotide-binding]]